If you’re planning a holiday in Malta, island hopping is one of the best ways to experience everything the Maltese Islands have to offer.
The beauty of island hopping in Malta is that no two trips are ever quite the same. Sea conditions, the season, and even the time of day can completely change your experience. While many visitors simply book the first available cruise, locals know that choosing the right route and the right skipper makes all the difference.
At GOZOblu Private Boat Tours, we have spent a lifetime exploring these waters. Our licenced local skippers don’t just follow a fixed timetable; they tailor every trip to the day’s conditions. Every private boat includes transparent pricing with fuel and port fees included, along with light local snacks on board, so you can simply relax and enjoy the journey.
Whether you’re looking for a Gozo and Comino tour, a private boat tour in Malta, or a full day of Malta island hopping, these are the best routes to consider.
Route 1: The Classic Gozo and Comino Island Hopping Tour
Best for: First-time visitors, families, couples, and anyone wanting to experience Malta’s most famous coastal attractions.
If you’re only planning one day on the water, this is the route we recommend most often. Combining Comino’s crystal-clear lagoons with Gozo’s dramatic coastline and rich history, it offers the perfect balance of swimming, sightseeing, and relaxation.
A typical itinerary includes:
- Depart from Gozo or northern Malta
- Cruise along Comino’s spectacular coastline
- Swim at the Blue Lagoon before the crowds arrive
- Explore Crystal Lagoon
- Visit the sea caves around Comino
- Continue to Gozo’s coastline
- Stop for lunch or sightseeing in Gozo
- Return with scenic coastal views
Blue Lagoon: Malta’s Most Famous Swimming Spot
No list of the best Malta island hopping routes would be complete without the Blue Lagoon. During summer, however, it also becomes one of Malta’s busiest attractions.
One of the biggest advantages of travelling with experienced local skippers is timing. Rather than arriving alongside dozens of other boats, GOZOblu plans departures to reach the Blue Lagoon early in the day whenever conditions allow. This gives guests a chance to enjoy calmer water, easier swimming, and a much more relaxed atmosphere.
Local tip: During July and August, the water is often at its clearest before 9:00 am. By late morning, the lagoon becomes considerably busier with ferries and larger cruise boats.
Crystal Lagoon: A Favourite Among Locals
Only a short cruise from the Blue Lagoon lies Crystal Lagoon, one of Comino’s hidden treasures. Because larger vessels cannot always access the best areas, smaller private boats often provide a more peaceful experience here.
If conditions are calm, your skipper may also take you through nearby sea caves where sunlight reflects beautifully off the water, creating some of the most impressive natural colours around Comino.
Discover Comino’s Sea Caves
Many visitors only associate Comino with the Blue Lagoon, but the island’s coastline hides countless caves, arches, and narrow passages that can only be explored by boat.
These include:
- Santa Marija Caves
- Crystal Lagoon caves
- Hidden limestone arches
- Quiet coves perfect for snorkelling
Continue to Gozo
After exploring Comino, the journey continues to Gozo, Malta’s greener and more traditional sister island.
Gozo offers a completely different atmosphere. Instead of busy beaches, you’ll find peaceful fishing villages, rolling countryside, historic landmarks, and welcoming local restaurants.
Depending on your chosen itinerary, you might visit:
- Victoria and the historic Citadel
- Ramla Bay, famous for its distinctive red-golden sand
- Mgarr ix-Xini
- Hondoq ir-Rummien
- Xlendi Bay
One of the benefits of booking with GOZOblu is the flexibility to customise your route. If you’d rather spend more time swimming than sightseeing or vice versa, your itinerary can often be adjusted around your preferences and the day’s sea conditions.
Route 2: Explore Comino’s Hidden Coves and Sea Caves
Best for: Snorkellers, photographers, couples, and visitors looking to escape the crowds.
While the Blue Lagoon is deservedly famous, some of Comino’s most memorable places receive far fewer visitors.
This route focuses on the quieter side of the island, taking you beyond the popular tourist spots to secluded bays and hidden coves that showcase Comino at its most natural.
Highlights include:
- Crystal Lagoon
- Santa Marija Bay
- Santa Marija Caves
- Elephant Rock
- Hidden snorkelling locations
- Scenic limestone cliffs
Santa Marija Bay
Located on Comino’s northern coast, Santa Marija Bay offers a peaceful alternative to the Blue Lagoon. The shallow, calm water makes it ideal for families, while its sheltered position often provides excellent swimming conditions even when other areas are busier.
Many visitors never discover this beautiful bay because larger commercial cruises tend to spend most of their time at the Blue Lagoon.
Elephant Rock
One of Comino’s lesser-known landmarks is Elephant Rock, a naturally formed limestone arch that resembles the shape of an elephant dipping its trunk into the sea.
Passing this impressive formation by boat offers fantastic photo opportunities and gives visitors a chance to appreciate the island’s rugged geology from a unique perspective.
Hidden Snorkelling Spots
For anyone interested in marine life, this is one of the best boat tours around Comino. The clear water around the island is home to colourful fish, underwater rock formations, and excellent visibility throughout much of the year.
Local tip: Summer mornings usually bring calmer seas before afternoon breezes develop. These early conditions often provide the clearest water for snorkelling and cave exploration.
Because GOZOblu operates flexible private charters rather than rigid group schedules, your skipper can choose the best swimming locations based on the day’s weather, helping you enjoy quieter spots that many visitors never get to experience.
Route 3: Malta’s South Coast Adventure
Best for: Photography enthusiasts, returning visitors, and travellers looking to discover a quieter side of Malta.
While most island-hopping itineraries focus on Gozo and Comino, Malta’s southern coastline deserves a place on every traveller’s list. This route showcases dramatic cliffs, sea caves, and hidden swimming spots that many visitors never see.
Highlights include:
- Blue Grotto: One of Malta’s most iconic natural attractions. Visiting by boat offers a completely different perspective from viewing it on land. On calm mornings, the water often acts like glass, creating perfect reflections and incredible photo opportunities.
- Dingli Cliffs (viewed from the sea): Standing over 200 metres above sea level, Dingli Cliffs are the highest point in Malta. As your boat cruises beneath the cliffs, you’ll appreciate the sheer scale of the landscape and discover caves and rock formations hidden below.
- Għar Lapsi: One of Malta’s favourite swimming spots among locals, a small inlet surrounded by rugged limestone coastline. The sheltered bay offers excellent snorkelling and wonderfully clear water. If you’re visiting during spring or autumn, this area is often peaceful enough to enjoy almost entirely to yourself.
- Hidden sea caves
- Quiet swimming bays
Route 4: Discover Gozo’s Spectacular Coastline
Best for: Nature lovers, history enthusiasts, and travellers wanting to explore beyond the typical tourist trail.
Many people visit Gozo for its charming villages and historic landmarks, but its coastline is equally spectacular. Exploring by boat allows you to reach secluded beaches, dramatic cliffs, and hidden valleys that are difficult or impossible to access by land.
Popular stops include:
- Dwejra Bay: Although the famous Azure Window collapsed in 2017, Dwejra remains one of Gozo’s most remarkable coastal destinations. Its dramatic rock formations, deep blue water, and rugged scenery continue to attract visitors from around the world.
- Inland Sea: Connected to the open Mediterranean by a naturally formed tunnel through the cliffs, the Inland Sea is one of Gozo’s most fascinating natural landmarks. Passing through the tunnel by boat is an unforgettable experience, revealing dramatic rock faces and open sea beyond.
- Wied il-Għasri: One of Gozo’s best-kept secrets. This narrow sea inlet is popular with snorkellers and divers thanks to its calm, crystal-clear water. It is also one of those places that many visitors never discover without local knowledge.
- Mgarr ix-Xini: A peaceful bay with calm water and a fascinating history. Mgarr ix-Xini was once used by fishermen and merchants; it is now a favourite swimming spot for locals and visitors seeking a quieter alternative to Malta’s more famous beaches.
- Hondoq ir-Rummien: Offers incredible views across to Comino and some of the clearest water in the Maltese Islands. Its sheltered location makes it an excellent stop for swimming, paddleboarding, and snorkelling.
One of the advantages of travelling with GOZOblu is the flexibility to combine several of these locations into one personalised itinerary. Rather than following a fixed route, your skipper can recommend the best stops based on the weather, sea conditions, and your interests, creating a day that feels completely your own.
Route 5: A Sunset Island-Hopping Cruise
Best for: Couples, special occasions, and anyone wanting to experience Malta from a different perspective.
There is something magical about being on the water as the sun begins to set over the Mediterranean.
As the day’s crowds return to shore, the coastline becomes quieter, and the changing light transforms the limestone cliffs into shades of gold, orange, and pink.
A typical sunset cruise may include:
- Evening swim in a quiet bay
- Scenic cruise past Comino or Gozo
- Coastal caves glowing in the late-afternoon light
- Spectacular sunset views across the Mediterranean
For many guests celebrating birthdays, anniversaries, or proposals, this becomes the highlight of their holiday.
Local tip: Summer evenings often bring calmer conditions after the heat of the day has eased, making sunset one of the most relaxing times to enjoy a private boat tour.
With GOZOblu, sunset charters are designed around your preferences. Whether you want to spend more time swimming, enjoy uninterrupted coastal views, or simply relax with light local snacks on board, the itinerary can be tailored to create an unforgettable experience.
Which Malta Island-Hopping Route Is Right for You?
Choosing the best route depends on the type of day you’re hoping to enjoy.
| If you want to… | Recommended Route |
| Visit Malta’s most famous attractions | Classic Gozo and Comino Tour |
| Escape the crowds | Hidden Coves of Comino |
| Discover dramatic coastal scenery | Malta’s South Coast Adventure |
| Explore Gozo’s hidden coastline | Around Gozo by Boat |
| Celebrate a special occasion | Sunset Island Hopping Cruise |
| Enjoy the best snorkelling | Hidden Coves of Comino |
| Experience history and culture | Classic Gozo and Comino Tour |
| Spend a relaxed day on a private boat | Any customised GOZOblu charter |
The biggest advantage of choosing a private charter is flexibility. Instead of rushing between scheduled stops, you can spend more time where you’re enjoying yourself most.
GOZOblu specialises in creating personalised experiences that combine the highlights of Gozo and Comino with hidden locations that many larger tour operators simply can’t include. With expert local skippers, transparent all-inclusive pricing that covers fuel and port fees, and light local snacks served on board, every trip is designed to feel relaxed, authentic, and tailored to you.
Local Tips for the Perfect Malta Island Hopping Adventure
After spending a lifetime on these waters, we’ve learned that a few simple decisions can completely transform your day at sea. These are the tips our skippers regularly share with guests before they step aboard.
- Start Early: If you’re planning to visit the Blue Lagoon during summer, an early departure is one of the best decisions you can make. Arriving before the larger tour boats gives you time to swim, snorkel, and enjoy the lagoon while it’s still relatively peaceful. As the morning progresses, the area naturally becomes much busier.
- Let the Weather Guide Your Route: Wind direction and swell can affect which bays offer the calmest water. Instead of following a rigid route, our skippers adapt the day to suit the weather, helping you enjoy safer swimming, clearer water, and quieter anchorages whenever possible.
- Don’t Rush Every Stop: Rather than spending only a few minutes at each location, allow yourself time to swim, snorkel, relax, and appreciate the scenery. Some of the most memorable moments happen in the quieter bays between the famous landmarks.
- Pack the Essentials: To make the most of your island hopping adventure, we recommend bringing swimwear, a towel, reef shoes, sunscreen, sunglasses, a hat, a waterproof phone case, and snorkelling equipment if you prefer to use your own.
If you’re joining a GOZOblu private charter, light local snacks, snorkelling gears, and bottled water are provided on board, making it easy to relax between swimming stops.
When Is the Best Time to Go Island Hopping in Malta?
Malta’s boating season runs for much of the year, but each season offers a slightly different experience.
- Spring (March to May): Spring brings mild temperatures, quieter anchorages, and beautiful coastal scenery. It’s an excellent time for sightseeing, photography, and relaxed boat trips before the summer crowds arrive.
- Summer (June to August): Summer is the busiest time for island hopping, with warm sea temperatures that are perfect for swimming. If you’re travelling during these months, we recommend setting off early to enjoy popular locations such as the Blue Lagoon before they become crowded.
- Autumn (September to October): Many locals consider autumn one of the best times to explore Malta by boat. The sea remains pleasantly warm after summer, visitor numbers begin to decrease, and the weather is often ideal for full-day trips around Gozo and Comino.
- Winter (November to February): Boat trips are still possible during suitable weather, although conditions are more changeable and some services operate less frequently. Private charters offer greater flexibility during winter because routes can be adjusted according to the forecast.
Frequently Asked Questions
Yes. A full-day boat trip allows plenty of time to swim in Comino’s famous lagoons before continuing to Gozo for sightseeing, lunch, or additional swimming stops.
If you value flexibility, quieter swimming spots, and a more personalised experience, a private charter is an excellent choice. You can spend more time at your favourite locations and adjust the itinerary throughout the day.
They offer completely different experiences. Comino is famous for its turquoise lagoons, sea caves, and swimming, while Gozo is known for its historic towns, scenic coastline, and slower pace of life. Many visitors choose to experience both islands in a single day.
Absolutely. One of the advantages of booking with GOZOblu is the flexibility to personalise your itinerary. Depending on sea conditions and your interests, your skipper can recommend hidden coves, scenic viewpoints, and quieter swimming locations that aren’t included on standard group tours.
A full-day trip offers the best balance, giving you enough time to explore Gozo and Comino without feeling rushed. Shorter half-day trips are also ideal if you’d like to focus on one island.
Discover Malta the Local Way with GOZOblu
The Maltese Islands are full of incredible places, but the best experiences rarely come from following the crowds. They’re found in the quiet coves, hidden sea caves, and peaceful swimming spots that lifelong locals have been enjoying for generations.
That’s exactly what GOZOblu aims to share with every guest.
Whether you’re planning a classic Gozo and Comino tour, a relaxed day discovering hidden bays, or a fully customised private boat tour in Malta, our experienced local skippers will help you experience the islands at their very best.
Every GOZOblu charter includes:
- Expert local skippers with lifelong knowledge of Malta, Gozo and Comino
- Flexible itineraries tailored to the day’s sea conditions and your preferences
- Transparent all-inclusive pricing with fuel and port fees included
- Light local snacks served on board
- The opportunity to combine Gozo and Comino in one unforgettable trip
Ready to explore Malta beyond the guidebooks?
Book your next island-hopping adventure with GOZOblu and discover the hidden beauty of Gozo, Comino, and the Maltese coastline with people who know these waters best.
About the Author: Captain Francesco
Francesco is a licensed skipper and co-founder of GOZOblu, born and raised in Nadur, Gozo. Growing up on the Gozitan coastline, Francesco spent his childhood spearfishing, swimming, and exploring the hidden coves and bays of the Maltese islands with his family. He knows every secret spot around Gozo and Comino — the kind of local knowledge that only comes from a lifetime on the water. Today, he shares that passion with guests on every GOZOblu private charter.
